Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Abstract

BackgroundEvolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1–8), their spatial and temporal expression profiles, potential upstream regulators and target genes.ResultsWe extracted all known human RFX1–8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1–3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes.ConclusionsThe wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4564-6) contains supplementary material, which is available to authorized users.

Differentiation of ciliated human midbrain-derived LUHMES neurons

“…The activity Z-value of ‘RFX3_RFX2’ strongly increased during LUHMES neuronal differentiation until d5, a signature very similar to the upregulated expression patterns of many ciliary genes ( Figure 8D; Supplementary Figure S2) . RFX transcription factors are known to be key ciliogenic regulators in many different organisms (Senti and Swoboda, 2008; Piasecki et al, 2010; Choksi et al, 2014; Sugiaman-Trapman et al, 2018). As an example, the ciliary gene BBS1, commonly involved in a ciliopathy with brain phenotypes – Bardet-Biedl Syndrome (Mykytyn et al, 2002), was also upregulated until d5 ( Supplementary Figure S2G ).…”

“…These results suggest that during LUHMES neuronal differentiation RFX2 might be responsible for the induction of ciliogenesis early on, while RFX3 is responsible for ciliary maintenance later on. We are aware of possible redundancies though, given that the human RFX transcription factor family consists of 8 members (Sugiaman-Trapman et al, 2018) and that RFX binding motifs (X-boxes) from the different family members are very similar to each other ( Figure 8D ).…”

Tensor decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis

“…REST is a master regulator of neurogenesis (10). RFX5 is known to be expressive in fetal brain (20). STAT3 promotes brain metastasis (14).…”

Parkinson-associatedSNCAenhancer variants revealed by open chromatin in mouse dopamine neurons

“…Of these, the Rfx family had not previously been implicated in DA neuron biology. Although several of the Rfx family members have been annotated as having expression in the cerebellum or fetal brain 43 , a role specifically in MB DA neurons has not previously been appreciated. By contrast, Nr4a2 is canonically associated with MB DA neurons 25,26 , is highly expressed in this population (139 RPKM), and was prioritized as a TF conferring regulatory potential in these cells; however, TF footprinting fails to provide evidence supporting its activity.…”